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- PDB-3pzv: C2 crystal form of the endo-1,4-beta-glucanase from Bacillus subt... -

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Basic information

Entry
Database: PDB / ID: 3pzv
TitleC2 crystal form of the endo-1,4-beta-glucanase from Bacillus subtilis 168
ComponentsEndoglucanaseCellulase
KeywordsHYDROLASE / alpha/beta barrel / glycosyl hydrolase / cellulose binding
Function / homology
Function and homology information


glucan catabolic process / cellulose binding / beta-glucosidase activity / cellulase / cellulase activity / cellulose catabolic process / cell surface / extracellular region
Similarity search - Function
Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) ...Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.867 Å
AuthorsSantos, C.R. / Paiva, J.H. / Akao, P.K. / Meza, A.N. / Silva, J.C. / Squina, F.M. / Ward, R.J. / Ruller, R. / Murakami, M.T.
CitationJournal: Biochem.J. / Year: 2012
Title: Dissecting structure-function-stability relationships of a thermostable GH5-CBM3 cellulase from Bacillus subtilis 168.
Authors: Santos, C.R. / Paiva, J.H. / Sforca, M.L. / Neves, J.L. / Navarro, R.Z. / Cota, J. / Akao, P.K. / Hoffmam, Z.B. / Meza, A.N. / Smetana, J.H. / Nogueira, M.L. / Polikarpov, I. / Xavier-Neto, ...Authors: Santos, C.R. / Paiva, J.H. / Sforca, M.L. / Neves, J.L. / Navarro, R.Z. / Cota, J. / Akao, P.K. / Hoffmam, Z.B. / Meza, A.N. / Smetana, J.H. / Nogueira, M.L. / Polikarpov, I. / Xavier-Neto, J. / Squina, F.M. / Ward, R.J. / Ruller, R. / Zeri, A.C. / Murakami, M.T.
History
DepositionDec 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase
B: Endoglucanase
C: Endoglucanase
D: Endoglucanase


Theoretical massNumber of molelcules
Total (without water)144,5934
Polymers144,5934
Non-polymers00
Water54030
1
A: Endoglucanase


Theoretical massNumber of molelcules
Total (without water)36,1481
Polymers36,1481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoglucanase


Theoretical massNumber of molelcules
Total (without water)36,1481
Polymers36,1481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Endoglucanase


Theoretical massNumber of molelcules
Total (without water)36,1481
Polymers36,1481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Endoglucanase


Theoretical massNumber of molelcules
Total (without water)36,1481
Polymers36,1481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)155.359, 81.080, 114.270
Angle α, β, γ (deg.)90.00, 104.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Endoglucanase / Cellulase / Carboxymethyl-cellulase / CMCase / Cellulase / Endo-1 / 4-beta-glucanase


Mass: 36148.203 Da / Num. of mol.: 4 / Fragment: catalytic domain, Unp residues 27-332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: eglS, bglC, gld, BSU18130 / Production host: Escherichia coli (E. coli) / References: UniProt: P10475, cellulase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG3350 200 mM sodium Nitrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 2.867→41.5 Å / Num. all: 57202 / Num. obs: 30407 / % possible obs: 97.1 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.9→3 Å / % possible all: 83.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.867→41.464 Å / SU ML: 0.41 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2961 1456 5.1 %
Rwork0.23 --
all0.245 28575 -
obs0.2335 28575 89.8 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.056 Å2 / ksol: 0.288 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-18.1486 Å20 Å210.0562 Å2
2---6.2013 Å20 Å2
3----11.9473 Å2
Refinement stepCycle: LAST / Resolution: 2.867→41.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9368 0 0 30 9398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069584
X-RAY DIFFRACTIONf_angle_d1.26112996
X-RAY DIFFRACTIONf_dihedral_angle_d16.2353452
X-RAY DIFFRACTIONf_chiral_restr0.0881376
X-RAY DIFFRACTIONf_plane_restr0.0061684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.867-2.96930.4494750.32031729X-RAY DIFFRACTION57
2.9693-3.08810.37791370.322383X-RAY DIFFRACTION80
3.0881-3.22860.36061380.28582679X-RAY DIFFRACTION89
3.2286-3.39880.35441650.27162776X-RAY DIFFRACTION93
3.3988-3.61160.28871490.26472833X-RAY DIFFRACTION94
3.6116-3.89030.32321650.2372905X-RAY DIFFRACTION96
3.8903-4.28140.25561360.20772917X-RAY DIFFRACTION96
4.2814-4.90010.27641640.20012937X-RAY DIFFRACTION97
4.9001-6.17040.28511490.23472966X-RAY DIFFRACTION97
6.1704-41.46840.27381780.20272994X-RAY DIFFRACTION97

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